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In tropically-adapted beef heifers, application of genomic prediction for age at puberty has been limited due to low prediction accuracies. Our aim was to investigate novel methods of pre-selecting whole-genom...
Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we as...
Estimating the genetic component of a complex phenotype is a complicated problem, mainly because there are many allele effects to estimate from a limited number of phenotypes. In spite of this difficulty, line...
In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed...
The single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) is one of the single-step evaluations that enable a simultaneous analysis of phenotypic and pedigree information of ge...
An amendment to this paper has been published and can be accessed via the original article.
The original article was published in Genetics Selection Evolution 2019 51:45
Environmental variance (VE) is partly under genetic control and has recently been proposed as a measure of resilience. Unravelling the genetic background of the VE of complex traits could help to improve resilien...
A multi-population genomic prediction (GP) model in which important pre-selected single nucleotide polymorphisms (SNPs) are differentially weighted (MPMG) has been shown to result in better prediction accuracy...
Control of the environmental variability by genetic selection offers possibilities for new selection objectives for productive traits. This methodology aims at reducing heterogeneity in productive traits and h...
Production and health traits are central in cattle breeding. Advances in next-generation sequencing technologies and genotype imputation have increased the resolution of gene mapping based on genome-wide assoc...
For assembling large whole-genome sequence datasets for routine use in research and breeding, the sequencing strategy should be adapted to the methods that will be used later for variant discovery and imputati...
The coupling of appropriate sequencing strategies and imputation methods is critical for assembling large whole-genome sequence datasets from livestock populations for research and breeding. In this paper, we ...
Bayesian regression models are widely used in genomic prediction, where the effects of all markers are estimated simultaneously by combining the information from the phenotypic data with priors for the marker ...
Polyploidy is widespread in animals and especially in plants. Different kinds of ploidies exist, for example, hexaploidy in wheat, octaploidy in strawberries, and diploidy, triploidy, tetraploidy, and pseudo-t...
Bovine paratuberculosis is a contagious disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), with adverse effects on animal welfare and serious economic consequences. Published results on host ge...
Skeletal damage is a challenge for laying hens because the physiological adaptations required for egg laying make them susceptible to osteoporosis. Previously, we showed that genetic factors explain 40% of the...
Transforming large amounts of genomic data into valuable knowledge for predicting complex traits has been an important challenge for animal and plant breeders. Prediction of complex traits has not escaped the ...
Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturi...
Physical removal of individuals from groups causes reductions in group sizes and changes in group composition, which may affect the predictive ability of estimates of indirect genetic effects of animals on phe...
Genomic prediction (GP) is a method whereby DNA polymorphism information is used to predict breeding values for complex traits. Although GP can significantly enhance predictive accuracy, it can be expensive an...
Breeding genetically hornless, i.e. polled, cattle provides an animal welfare-friendly and non-invasive alternative to the dehorning of calves. However, the molecular regulation of the development of horns in ...
Most fish breeding programs aim at improving growth rate and include feed conversion ratio (FCR) neither in the breeding goal nor in the selection index, although decreasing FCR is known to increase farm profi...
In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated...
Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variab...
The availability of both pedigree and genomic sources of information for animal breeding and genetics has created new challenges in understanding how they can be best used and interpreted. This study estimated...
Tibetan Terrier is a popular medium-sized companion dog breed. According to the history of the breed, the western population of Tibetan Terriers includes two lineages, Lamleh and Luneville. These two lineages ...
Inbreeding is caused by mating between related individuals and its most common consequence is inbreeding depression. Several studies have detected heterogeneity in inbreeding depression among founder individua...
During the last decade, the use of common-variant array-based single nucleotide polymorphism (SNP) genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic...
The main aim of single-step genomic predictions was to facilitate optimal selection in populations consisting of both genotyped and non-genotyped individuals. However, in spite of intensive research, biases st...
The dimensionality of genomic information is limited by the number of independent chromosome segments (Me), which is a function of the effective population size. This dimensionality can be determined approximatel...
Controlled mating procedures are widely accepted as a key aspect of successful breeding in almost all animal species. In honeybees, however, controlled mating is hard to achieve. Therefore, there have been sev...
Hamiltonian Monte Carlo is one of the algorithms of the Markov chain Monte Carlo method that uses Hamiltonian dynamics to propose samples that follow a target distribution. The method can avoid the random walk...
Whole-genome sequence (WGS) data could contain information on genetic variants at or in high linkage disequilibrium with causative mutations that underlie the genetic variation of polygenic traits. Thus far, g...
In honey bees, observations are usually made on colonies. The phenotype of a colony is affected by the average breeding value for the worker effect of the thousands of workers in the colony (the worker group) ...
As one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, the genetic loci that underlie phenotypic variations in domestic ...
After publication of original article [1], the authors noticed that there was an error.
The original article was published in Genetics Selection Evolution 2018 50:53
After publication of this work [1], we noticed that there was an error: the formula to calculate the standard error of the estimated correlation
The original article was published in Genetics Selection Evolution 2019 51:50
For infectious diseases, the probability that an animal gets infected depends on its own susceptibility, and on the number of infectious herd mates and their infectivity. Together with the duration of the infe...
The detection of regions that affect quantitative traits (QTL), to implement selection assisted by molecular information, remains of particular interest in dairy sheep for which genetic gain is constrained by ...
Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy...
Following publication of original article [1], we noticed that there was an error: Eq. (3) on page 5 is the genomic relationship matrix that
The original article was published in Genetics Selection Evolution 2019 51:38
White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein–Friesian cattle, and several previous studies have detected gen...
Two distinct populations have been extensively studied in Atlantic cod (Gadus morhua L.): the Northeast Arctic cod (NEAC) population and the coastal cod (CC) population. The objectives of the current study were t...
The pig breeding industry has undergone a large number of mergers in the past decades. Various commercial lines were merged or discontinued, which is expected to reduce the genetic diversity of the pig species...
Ribosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes....
For genomic selection in populations with a small reference population, combining populations of the same breed or populations of related breeds is an effective way to increase the size of the reference popula...
Multi-trait single step genetic evaluation is increasingly facing the situation of having more individuals with genotypes than markers within each genotype. This creates a situation where the genomic relations...
Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked red...
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Genetics Selection Evolution